Gallery

This gallery presents example results of modeling using different flexibility modes for various proteins, cases, or folds to illustrate how the modes work. Please pay attention to the legend, which shows the level of flexibility in Ångströms. The examples below include links to the corresponding jobs, allowing for a more detailed exploration of each case:

• an example of a potassium channel using the input file: PDB: 1BL8

  

  Flexibility mode: flexible.
  Job link: https://lcbio.pl/cabsflex3/job/91b25de96f1d9b/

  Flexibility mode: rigid.
  Job link: https://lcbio.pl/cabsflex3/job/febb8774287f09/

• an example of a tyrosine kinase domain using the input file: PDB: 1IRK

  

  Flexibility mode: flexible.
  Job link: https://lcbio.pl/cabsflex3/job/7f17efe6b04f8b/

  Flexibility mode: rigid.
  Job link: https://lcbio.pl/cabsflex3/job/7b713b97d0a074

• an example of a Rossmann-like/ tRNA synthetase fold: PDB: 1ECL

  

  Flexibility mode: flexible.
  Job link: https://lcbio.pl/cabsflex3/job/25df30920e0086/

  Flexibility mode: rigid.
  Job link: https://lcbio.pl/cabsflex3/job/b8b1c4b0427545/

• an example of a Trypsin-like serine protease: PDB: 1AO5

  

  Flexibility mode: flexible.
  Job link: https://lcbio.pl/cabsflex3/job/29d65e9c55a888/

  Flexibility mode: rigid.
  Job link: https://lcbio.pl/cabsflex3/job/b1bbd4f0671ce1/

• an example of an Immunoglobulin fold: PDB: 1IGT

  

  Flexibility mode: flexible.
  Job link: https://lcbio.pl/cabsflex3/job/40f6b02b9564ed/

  Flexibility mode: rigid.
  Job link: https://lcbio.pl/cabsflex3/job/839fb9807a2ecb/

• Modeling loop flexibility: PDB: 1TGR

  

  Flexibility mode: rigid-pLDDT.
  Job link: https://lcbio.pl/cabsflex3/job/6e9db9e8217b9a/

  Flexibility mode: rigid.
  Job link: https://lcbio.pl/cabsflex3/job/3a89ed0be6d0b8/

  The loop region shows greater fluctuations in the Rigid-pLDDT simulation, because it was predicted with lower pLDDT score by AlphaFold. The pLDDT scores are available in the job link for simulation with Rigid-pLDDT flexibility mode.

• Dynamic fluctuations across different protein fragments: PDB: 2V4N

  

  Flexibility mode: rigid-pLDDT.
  Job link: https://lcbio.pl/cabsflex3/job/f3c2e0b103cfe4/

  Flexibility mode: rigid.
  Job link: https://lcbio.pl/cabsflex3/job/28dc78b9e410b3/

  In the Rigid simulation, the region exhibiting the greatest fluctuations is the double beta sheet. In contrast, the Rigid-pLDDT simulation - which incorporates pLDDT scores - shows the terminal alpha helix as the most flexible region. The pLDDT scores used in this simulation are available in the job link for the Rigid-pLDDT flexibility mode.

• Incorporating pLDDT scores allows the protein structure to exhibit greater flexibility: PDB: 3CW3

  

  Flexibility mode: rigid-pLDDT.
  Job link: https://lcbio.pl/cabsflex3/job/8a6fead2a49070/

  Flexibility mode: rigid.
  Job link: https://lcbio.pl/cabsflex3/job/fcff449f4d8328/

  Using pLDDT scores to construct restraints allows to capture the dynamic movements in the flexible regions while maintaining rigidity in the well-structured parts. The pLDDT scores used in this simulation are available in the job link for the Rigid-pLDDT flexibility mode.

• Modeling Flexibility of Intrinsically Disordered Regions and Proteins: PDB: 2LEJ

  

  Flexibility mode: flexible.
  Job link: https://lcbio.pl/cabsflex3/job/c3efa77f7e4271/

  Flexibility mode: rigid.
  Job link: https://lcbio.pl/cabsflex3/job/98de268524d378/

• Modeling Flexibility of Intrinsically Disordered Regions and Proteins: PDB: 2AN7

  

  Flexibility mode: rigid-pLDDT.
  Job link: https://lcbio.pl/cabsflex3/job/cb38856234264e/

• Modeling Flexibility of Intrinsically Disordered Regions and Proteins: PDB: 2K8P

  

  Flexibility mode: unleashed.
  Job link: https://lcbio.pl/cabsflex3/job/9571eb36dcd0fa/